cwlVersion: v1.2
label: "gp_makeblastdb"

class: Workflow
requirements:
- class: StepInputExpressionRequirement
    
inputs:
  asn_cache: Directory[]
  lds2: File?
  molecules: File?
  asnb: File?
  asnt: File?
  dbtype: string
  fasta: File?
  hardmask: File?
  softmask: File?
  title: string
  ids:  File?

steps:
  actual:
    run:
      class: CommandLineTool
      requirements:
          - class: InitialWorkDirRequirement
            listing:
              - entry: $(inputs.molecules)
                writable: False
    
      baseCommand: gp_makeblastdb
      arguments: [ -nogenbank  ]
      inputs:
        asn_cache:
          type: Directory[]
          inputBinding:
            prefix: -asn-cache
            itemSeparator: ","
        lds2:
          type: File?
          inputBinding:
              prefix: -lds2
        molecules:
          type: File?
        asnb:
          type: File?
          inputBinding:
              prefix: -asnb
        asnt:
          type: File?
          inputBinding:
              prefix: -asnt
        dbtype:
          type: string
          inputBinding:
              prefix: -dbtype
        fasta:
          type: File?
          inputBinding:
              prefix: -fasta
        found_ids_output_file:  #    -found-ids-output  out/found_ids.txt \
          type: string
          default: found_ids.txt
          inputBinding:
              prefix: -found-ids-output
        found_ids_output_manifest:  #    -found-ids-output-manifest  out/found_ids.mft \
          type: string
          default: found_ids.mft
          inputBinding:
             prefix: -found-ids-output-manifest
        hardmask: #    -hardmask-manifest  inp/hardmask_data.mft 
          type: File?
          inputBinding:
             prefix: -hardmask
        output_db_file:
          type: string
          default: blastdb
          inputBinding:
              prefix: -db
        output_db_manifest:
          type: string
          default: blastdb.mft
          inputBinding:
              prefix: -output-manifest
        softmask: #    -softmask-manifest  inp/softmask_data.mft \
          type: File?
          inputBinding:
              prefix: -softmask
        title:  #    -title  'BLASTdb  created by GPipe'
          type: string
          inputBinding:
              prefix: -title
        ids:
          type: File?
          inputBinding:
              prefix: -ids
      outputs:
        dbname: 
          type: string
          outputBinding: 
              outputEval: $(inputs.output_db_file)
        found_ids:
          type: File
          outputBinding:
              glob: $(inputs.found_ids_output_file)
        
        blastfiles:
          type: File[]
          outputBinding:
              glob: "blastdb.*"  #  string literal here must match ${output_db_file}             
    in:
      asn_cache: asn_cache
      asnb: asnb
      asnt: asnt
      dbtype: dbtype
      fasta: fasta
      hardmask: hardmask #    -hardmask-manifest  inp/hardmask_data.mft 
      softmask: softmask #    -softmask-manifest  inp/softmask_data.mft \
      title:  title #    -title  'BLASTdb  created by GPipe'
      ids: ids
    out: [blastfiles]
  mkdir:
    run:
      class: CommandLineTool
      requirements:
        - class: ShellCommandRequirement
      arguments:
        - shellQuote: false
          valueFrom: >-
            mkdir $(inputs.blastdir) && cp
      inputs:
        blastfiles:
          type: File[]
          inputBinding:
            position: 1
        blastdir:
          type: string
          inputBinding:
            position: 2

      outputs:
        blastdb:
          type: Directory
          outputBinding:
            glob: $(inputs.blastdir)
    in:
      blastfiles: actual/blastfiles
      blastdir: 
        default: blastdir
    out: [blastdb]    
  
outputs:
  blastdb:
    type: Directory
    outputSource: mkdir/blastdb

    
